Short activation domains control chromatin association of transcription factors

Transcription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. Despite evidence to the contrary, DBDs are often assumed to be the primary mediators of transcription factor (TF) interactions with DNA and chromatin. Here, we used fast single-molecule tracking of transcription factors in living cells to show that short activation domains can control the fraction of molecules bound to chromatin. Stronger activation domains have higher bound fractions and longer residence times on chromatin. Furthermore, mutations that increase activation domain strength also increase chromatin binding. This trend was consistent in four different activation domains and their mutants. This effect further held for activation domains appended to three different structural classes of DBDs. Stronger activation domains with high chromatin-bound fractions also exhibited increased binding to the p300 coactivator in proximity-assisted photoactivation experiments. Genome-wide measurements indicate these activation domains primarily control the occupancy of binding rather than the genomic location. Taken together, these results demonstrate that very short activation domains play a major role in tethering transcription factors to chromatin.